docs: def align_orthologous_genes_pairwise(self, gapopen=10, gapextend=0.5):
          """For each gene in the base strain, run a pairwise alignment for all orthologous gene sequences to it."""
          for ref_gene in tqdm(self.reference_gempro.genes):
              if len(ref_gene.protein.sequences) > 1:
                  alignment_dir = op.join(self.sequences_by_gene_dir, ref_gene.id)
                  if not op.exists(alignment_dir):
                      os.mkdir(alignment_dir)
                  ref_gene.protein.pairwise_align_sequences_to_representative(gapopen=gapopen, gapextend=gapextend,
                                                                              outdir=alignment_dir, parse=True)